Molecular Phylogenetics and Evolution最新文献_第6页

Evolution, range formation and a revised taxonomy of the disjunctly distributed European members of Astragalus sect. Caprini, an intricate group including highly endangered species of dry grasslands 黄芪科（Astragalus sect.Caprini是一个复杂的群体，包括干旱草原上的高度濒危物种。

IF 3.6 1区生物学 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY

Molecular Phylogenetics and Evolution

Pub Date : 2024-11-16 DOI: 10.1016/j.ympev.2024.108242

Clemens Maylandt , Philipp Kirschner , Daniela Pirkebner , Božo Frajman , Julio Peñas de Giles , Peter Schönswetter , Pau Carnicero

The Eurasian steppes are among the largest and most threatened biomes on Earth. During cold periods of the Pleistocene, the zonal Eurasian steppes had a much larger extent as compared to interglacial periods, and repeatedly expanded into large areas of present-day forested temperate Europe. Conversely, during warm periods, forest expansion recurrently forced Eurasian steppe biota into disjunct and small warm-stage refugia, i.e. today’s extrazonal steppes. The rare, threatened and disjunctly distributed northwestern African and European members of Astragalus sect. Caprini constitute an ideal model for gaining insights into the evolutionary dynamics of typical steppe biota. Here, we reconstructed the spatiotemporal diversification of northwestern African and European members of Astragalus sect. Caprini based on a combination of RADseq data, single gene markers (internal transcribed spacer, plastid ycf1), genome size measurements and multivariate morphometrics. We outline an evolutionary scenario in which the group originated in the Irano-Turanian region and started to diversify shortly after the Mid-Pleistocene-Transition (ca. 0.5 to 0.7 Ma). While lineages occurring in (sub-)mediterranean mountain ranges diverged early, lineages occurring in northern lowland steppes are much younger (ca. 0.2 to 0.3 Ma), emphasizing the importance of southern European mountain ranges as long-term refugia. Recurrent colonization of the western Mediterranean region by eastern Mediterranean lineages and secondary contacts of currently spatially isolated lineages have significantly (co-)shaped the genetic structure within the group; we assume that these events may be a consequence of cold-stage range expansions. Based on combined genetic and morphometric data, we suggest treating the ten lineages introduced in this study as independent species, contrasting previous taxonomic treatments.

欧亚大草原是地球上面积最大、受威胁最严重的生物群落之一。在更新世的寒冷时期，欧亚草原地带的范围比间冰期大得多，并一再扩展到今天温带欧洲森林覆盖的大片地区。相反，在温暖时期，森林的扩张经常迫使欧亚大草原生物群进入不连续性的小型温暖阶段避难所，即今天的地带外大草原。稀有、濒危和分布不均的西北非和欧洲黄芪科成员，构成了一个理想的黄芪研究模式。Caprini 是了解典型草原生物群进化动态的理想模型。在这里，我们根据黄芪科（Astragalus sect.这里，我们结合 RADseq 数据、单基因标记（内部转录间隔、质体 ycf1）、基因组大小测量和多元形态计量学，重建了非洲西北部和欧洲黄芪科成员的时空多样性。我们勾勒出这样一种进化情景：该类群起源于伊朗-都兰地区，在中更新世过渡（约 0.5 至 0.7 马年）后不久开始分化。发生在（亚）地中海山脉的世系分化较早，而发生在北部低地草原的世系分化则要年轻得多（约 0.2 至 0.3 Ma），这强调了南欧山脉作为长期避难所的重要性。地中海东部各系对地中海西部地区的反复殖民以及目前在空间上相互隔离的各系之间的二次接触极大地（共同）塑造了该类群的遗传结构；我们认为这些事件可能是寒冷阶段范围扩张的结果。根据遗传学和形态计量学的综合数据，我们建议将本研究中引入的 10 个品系视为独立的物种，与之前的分类学处理方法形成对比。

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引用次数: 0

Nuclear phylogenomics of Eperua (Leguminosae) highlights the role of habitat and morphological lability in dispersal and diversification across Amazonia and in the Caatinga-Cerrado ecotone Eperua（豆科）的核系统发生组学突显了栖息地和形态易变性在整个亚马孙和卡廷加--塞拉多生态区域的扩散和多样化中的作用。

IF 3.6 1区生物学 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY

Molecular Phylogenetics and Evolution

Pub Date : 2024-11-15 DOI: 10.1016/j.ympev.2024.108236

Elenice A. Fortes , Jacob B. Landis , Hans ter Steege , Chelsea D. Specht , Jeff J. Doyle , Vidal de F. Mansano

Eperua is a genus of Neotropical trees that forms a major component of tropical lowland forests in Amazonia, especially in the Guiana Shield and on white-sand forests. One species occurs in the Cerrado-Caatinga ecotone, and the genus also inhabits riverine and terra firme forests. Species in Eperua exhibit one of two drastically different floral architectures and inflorescence types, each associated with distinct pollinators. Prior phylogenetic studies of Eperua have revealed an unstructured topology concerning floral architectures and inflorescence types. In addition, no investigation has been conducted on how the evolution of these traits and habitat preferences influenced the dispersal and diversification of Eperua. Using target capture sequencing, we inferred the most comprehensive phylogeny for Eperua to date, sampling all 19 known species, five for the first time. We used coalescence, concatenation, and network methods to infer the Eperua phylogeny and investigate sources of incongruence impacting resolution and support. We reconstructed the biogeographic history and ancestral states for the flower architecture, inflorescence type, and habitat preference. Our phylogenomic analyses successfully resolved relationships within Eperua, attributing conflicts between the species tree and concatenated tree to gene tree discordance linked to reticulation events. Biogeographical analyses indicate that Eperua originated and initially diversified in the white-sand forests of the Guiana Shield. A subsequent adaptation to riverine and terra firme forests enabled Eperua to expand into new habitats and regions. Still, its historical preference for white-sand forests probably accounts for its absence in the southern and western parts of Amazonia. Ancestral geographic areas and corolla morphotype reconstructions suggest that speciation in Eperua has occurred in sympatry, likely driven by pollinator shifts mediated by drastic changes in floral architecture.

Eperua 是新热带树木的一个属，是亚马逊热带低地森林的主要组成部分，尤其是在圭亚那盾和白沙森林中。其中一个物种出现在塞拉多-卡廷加生态区，该属还栖息在河流和陆地森林中。Eperua 的物种有两种截然不同的花结构和花序类型，每种都与不同的授粉者有关。之前的 Eperua 系统发育研究显示，花结构和花序类型的拓扑结构并不稳定。此外，关于这些特征和栖息地偏好的进化如何影响 Eperua 的扩散和多样化，还没有进行过研究。通过目标捕获测序，我们推断出了迄今为止最全面的Eperua系统发生，对所有19个已知物种进行了取样，其中5个物种是首次发现。我们使用聚合、连接和网络方法来推断 Eperua 系统发生，并研究影响分辨率和支持率的不一致性来源。我们重建了花的结构、花序类型和栖息地偏好的生物地理历史和祖先状态。我们的系统发生学分析成功地解析了Eperua内部的关系，将物种树与连接树之间的冲突归因于与网状结构事件相关的基因树不一致。生物地理学分析表明，Eperua起源于圭亚那地盾的白沙森林，并在那里进行了最初的多样化。随后对河流和陆地森林的适应使Eperua得以扩展到新的栖息地和地区。不过，Eperua历来偏爱白沙森林，这可能是其在亚马逊南部和西部缺失的原因。始祖地理区域和花冠形态类型的重建表明，Eperua的物种变异发生在同域中，很可能是由授粉者的转移和花卉结构的急剧变化所引起的。

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引用次数: 0

Phylogenomic analyses shed new light on the spatiotemporal evolution of global larches: Implications for the dynamics of boreal forests 系统发生组分析为全球落叶松的时空演变提供了新线索：对北方森林动态的影响。

IF 3.6 1区生物学 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY

Molecular Phylogenetics and Evolution

Pub Date : 2024-11-15 DOI: 10.1016/j.ympev.2024.108240

Xiu-Fei Qiu , Yan-Yan Liu , Ge Wu , Cong-Hui Xu , Xin-Quan Liu , Xiao-Yan Xiang , Xiao-Xin Wei , Xiao-Quan Wang

As the Earth warms, understanding the long-term dynamics of forest ecosystems is essential for guiding forest management and biodiversity conservation. Insights from past dynamics may provide valuable lessons for managing today’s forests. Here, we investigated the spatiotemporal evolution of global larches to gain further insights into how boreal forests change over time. We first reconstructed a highly resolved and robust phylogeny of Larix covering all widely recognized species, using both transcriptome-based 1,301 orthologous genes (OGs) and plastid genomes. In sharp contrast to previous studies, an unexpected deep split between the circumboreal and Qinghai-Tibetan Plateau (QTP) larches was revealed in our study. Within each lineage, two geographically distinct clades were further resolved. Biogeographical analyses suggest that Larix might have an origin of Eocene in high-latitude uplands, and during the Miocene, all extant species have appeared. Cenozoic climate- and orogeny-triggered vicariance likely played a major role in the divergence of global larches. Our results also demonstrate that the proto-boreal forest biome may have a relatively old origin back to the early Miocene, and significant winnowing and species alteration would have occurred as the climate shifted to much colder and drier conditions during the Neogene. Ecological niche analyses show various responses of the circumboreal and QTP larches under different climate scenarios, but both lineages are negatively impacted by warming climates. These findings have important conservation implications given the sensitivity of boreal forests in the face of global warming. Our work further emphasizes the importance of a solid phylogenetic framework for evolutionary and biogeographical inferences.

随着地球变暖，了解森林生态系统的长期动态对于指导森林管理和生物多样性保护至关重要。从过去的动态中获得的启示可能会为今天的森林管理提供宝贵的经验。在这里，我们研究了全球落叶松的时空演化，以进一步了解北方森林是如何随时间变化的。我们首先利用基于转录组的 1,301 个直向同源基因（OGs）和质体基因组，重建了一个高度解析和稳健的拉里克系统发育，涵盖了所有公认的物种。与之前的研究形成鲜明对比的是，我们的研究发现，在环周和青藏高原（QTP）落叶松之间出现了意想不到的深度分裂。在每一系中，又进一步分出了两个地理上不同的支系。生物地理学分析表明，落叶松可能起源于始新世的高纬度高地，在中新世出现了所有现存物种。新生代气候和造山运动引发的沧海桑田可能在全球落叶松的分化中扮演了重要角色。我们的研究结果还表明，原生林生物群落的起源可能要追溯到中新世早期，随着新近纪气候变得更加寒冷和干旱，原生林生物群落会发生重大的筛选和物种改变。生态位分析表明，在不同的气候情景下，环坡落叶松和QTP落叶松会有不同的反应，但这两个品系都会受到气候变暖的负面影响。鉴于北方森林对全球变暖的敏感性，这些发现对保护具有重要意义。我们的工作进一步强调了坚实的系统发生学框架对于进化和生物地理推断的重要性。

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引用次数: 0

Phylogenomic analyses of hamsters (Cricetinae) inferred from GBS data and mitochondrial genomes 根据 GBS 数据和线粒体基因组推断的仓鼠（Cricetinae）系统进化分析。

IF 3.6 1区生物学 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY

Molecular Phylogenetics and Evolution

Pub Date : 2024-11-14 DOI: 10.1016/j.ympev.2024.108241

Xuan Pan , Xuming Wang , Yingxun Liu , Yuchun Li , Rui Liao , Zhongzheng Chen , Buqing Peng , Xichao Zhu , Jiatang Li , Shaoying Liu

Accurate species delimitation and identification is crucial for species conservation, providing a foundation for studies on evolutionary biology, ecology, and essentially all biological disciplines. The subfamily Cricetinae (Cricetidae, Rodentia), known as hamsters, is widely distributed in the Palearctic region. At present, there are nine genera and 18 species of hamsters are recognized worldwide, although the taxonomic status of certain taxa remains unclear. In this study, we collected 146 hamster specimens representing 14 species and generated new mitochondrial genomes and nuclear genome-wide single nucleotide polymorphisms (SNPs) to explore their relationships among these hamsters using multiple species delimitation approaches. Results showed: (1) strong phylogenetic support for the classification of Urocricetus, Nothocricetulus, and Cansumys as separate genera; (2) Urocricetus contained two separate species, U. kamensis and U. lama, with U. alticola and U. tibetanus considered synonyms of U. lama; (3) U. kamensis and U. lama are separated by the Nujiang River, with the matching divergence time suggesting that the formation of the river was the primary evolutionary factor driving the species differentiation, and (4) genetic differentiation occurred within the Tscherskia genus, which included two cryptic species.

准确的物种划分和鉴定对于物种保护至关重要，它为进化生物学、生态学以及基本上所有生物学科的研究提供了基础。仓鼠亚科（Cricetinae，Rodentia）被称为仓鼠，广泛分布于古北地区。目前，全世界公认的仓鼠有 9 属 18 种，但某些类群的分类地位仍不明确。在这项研究中，我们收集了代表 14 个种的 146 只仓鼠标本，并生成了新的线粒体基因组和核基因组单核苷酸多态性（SNPs），利用多种物种划分方法探讨了这些仓鼠之间的关系。结果显示(1) Urocricetus、Nothocricetulus 和 Cansumys 作为独立属的分类得到了强有力的系统发育支持；(2) Urocricetus 包含两个独立的种，即 U. kamensis 和 U. lama，其中 U. alticola 和 U. tibetanus 被认为是 U. lama 的异名；(3) U. kamensis 和 U. lama 被怒江大峡谷分隔开来。lama 被怒江分隔开来，两者的分化时间相吻合，表明怒江的形成是物种分化的主要进化因素；（4）Tscherskia 属内部发生了遗传分化，其中包括两个隐性物种。

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引用次数: 0

Reticulate Evolution in Japanese Sceptridium (Ophioglossaceae), including diploid, tetraploid, and hexaploid species 日本蛇尾草（Ophioglossaceae）的网状进化，包括二倍体、四倍体和六倍体物种。

IF 3.6 1区生物学 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY

Molecular Phylogenetics and Evolution

Pub Date : 2024-11-14 DOI: 10.1016/j.ympev.2024.108244

Sousuke Ishii , Norio Sahashi , Atushi Ebihara , Shun K. Hirota , Yoshihisa Suyama , Yasuyuki Watano

Homospory represents an intriguing reproductive strategy, including the potential for gametophytic selfing, considered the ultimate form of selfing. The plants of the fern genus Sceptridium (Ophioglossaceae) are generally considered to be predominantly selfing, making them suitable for analyzing speciation patterns and intraspecific variation characteristic of homosporous plants. The Sceptridium species in Japan not only exhibit variations in ploidy, including diploids, tetraploids, and hexaploids, but also pose taxonomic challenges due to morphologically distinctive forms that are difficult to be assigned to previously described species. We developed multiple single-copy nuclear markers and aimed to identify ancestral species of the polyploids and to elucidate the evolutionary entity of an undescribed species. Chromosome counts and analyses of individual gene trees confirmed that S. japonicum, S. atrovirens, and the undescribed species are allohexaploids originating through hybridization between a maternal tetraploid ancestor closely related to S. formosanum and a paternal diploid ancestor closely related to extant diploid species. By identifying homoeologs derived from the diploid ancestor, we successfully analyzed the phylogenetic relationship between the diploid ancestor of the hexaploid species and extant diploid species using the multispecies coalescent model. The examined undescribed species could not be distinguished from S. atrovirens by multiple nuclear markers or by SNP data obtained from multiplexed ISSR genotyping by sequencing. This species appears to represent one of the polymorphisms of S. atrovirens, which was fixed through gametophytic selfing.

同株繁殖是一种引人入胜的繁殖策略，包括配子自交的可能性，配子自交被认为是自交的最终形式。蕨类植物蛇尾蕨属（Ophioglossaceae）的植物通常被认为以自交为主，因此适合分析同孢植物特有的物种演化模式和种内变异。日本的蛇床子属（Sceptridium）物种不仅在倍性上存在差异，包括二倍体、四倍体和六倍体，而且在分类学上也存在挑战，因为它们在形态上各具特色，很难归入以前描述的物种。我们开发了多个单拷贝核标记，旨在确定多倍体的祖先物种，并阐明一个未描述物种的进化实体。染色体计数和个体基因树分析证实，日本蓟马、阿特罗维林蓟马和未被描述的物种都是异源六倍体，起源于母系四倍体祖先（与福美双密切相关）和父系二倍体祖先（与现存二倍体物种密切相关）之间的杂交。通过鉴定源自二倍体祖先的同源物，我们成功地利用多物种凝聚模型分析了六倍体物种的二倍体祖先与现存二倍体物种之间的系统发育关系。通过多个核标记或多重 ISSR 基因分型测序获得的 SNP 数据，我们无法将该未描述物种与 S. atrovirens 区分开来。该物种似乎代表了 S. atrovirens 的多态性之一，它通过配子体自交而固定下来。

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引用次数: 0

A phylogenomic tree of wood-warblers (Aves: Parulidae): Dealing with good, bad, and ugly samples 啄木鸟（鸟类：Parulidae）的系统发生树：处理好、坏、丑样本。

IF 3.6 1区生物学 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY

Molecular Phylogenetics and Evolution

Pub Date : 2024-11-13 DOI: 10.1016/j.ympev.2024.108235

Min Zhao , Jessica A. Oswald , Julie M. Allen , Hannah L. Owens , Peter A. Hosner , Robert P. Guralnick , Edward L. Braun , Rebecca T. Kimball

The New World warblers (Parulidae) are a model group for ecological and evolutionary analyses. However, current phylogenetic relationships across this family are based upon few loci. Here we use ultraconserved elements (UCEs) to estimate a rigorous species-level phylogeny for the family. As is true for many groups, high-quality tissues were unavailable for some taxa. Thus, we explored methods for incorporating sequences derived from historical (toe pad) samples to expand the phylogenetic datasets. We recovered an average of 4,186 UCE loci and mitochondrial bycatch data (supplemented with published mitochondrial data) from 96% of all currently recognized species. We found that the UCE phylogeny built with alignments with less than 70% of gaps and ambiguities recovered the most robust phylogenetic relationships for this family, representing 101 species. Using this phylogeny as a topological backbone and adding ten fair quality “bad” samples effectively generated an overall well supported phylogeny, representing 108 species (∼90% of all species). Based on this tree, we then added in seven poor quality “ugly” samples and six of those were placed within their expected genera. We also explored the phylogenetic positions of the likely extinct Leucopeza semperi and the endangered Catharopeza bishopi where limited data was obtained. Overall, taxonomic placements in our UCE trees largely correspond to previously published studies with the recovery of all currently recognized genera as monophyletic except for Basileuterus which was rendered paraphyletic by B. lachrymosus. Our study provides insights in understanding the phylogenetic relationships of a model Passeriformes family and outlines effective practices for managing sparse genomic data sourced from historical museum specimens. Variable topological arrangements across datasets and analyses reflect the evolutionary complexity of this group and provide future topics for in-depth studies.

新世界莺科（Parulidae）是生态学和进化分析的典范类群。然而，目前该科的系统发生关系仅基于少数位点。在这里，我们使用超保守元素（UCE）来估算该科严格的物种水平系统发生。与许多类群一样，一些类群无法获得高质量的组织。因此，我们探索了从历史（趾垫）样本中获取序列的方法，以扩展系统发生学数据集。我们从目前所有已确认物种中的 96% 恢复了平均 4,186 个 UCE 位点和线粒体旁系亲属数据（辅以已发表的线粒体数据）。我们发现，用缺口和模糊性小于 70% 的排列建立的 UCE 系统发生恢复了该科最稳健的系统发生关系，代表了 101 个物种。将这一系统发生作为拓扑骨干，并添加 10 个质量一般的 "坏 "样本，有效地生成了一个总体支持良好的系统发生，代表 108 个物种（占所有物种的 90%）。在此系统树的基础上，我们又加入了 7 个质量较差的 "丑陋 "样本，其中 6 个样本被归入了预期的属。我们还探讨了可能已经灭绝的 Leucopeza semperi 和濒危的 Catharopeza bishopi 的系统发育位置，因为我们获得的数据有限。总体而言，我们的 UCE 树中的分类位置与之前发表的研究结果基本一致，除了 Basileuterus 被 B. lachrymosus 变成旁系外，所有目前公认的属都恢复了单系。我们的研究为了解一个典型的雀形目家族的系统发生关系提供了深入的见解，并为管理从博物馆历史标本中获取的稀少基因组数据提供了有效的方法。不同数据集和分析中的拓扑结构变化反映了该类群进化的复杂性，并为今后的深入研究提供了课题。

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引用次数: 0

Unveiling hidden diversity: Phylogenomics of neotomine rodents and taxonomic implications for the genus Peromyscus 揭示隐藏的多样性：新啮齿动物的系统发生组学及对啮齿动物属分类学的影响。

IF 3.6 1区生物学 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY

Molecular Phylogenetics and Evolution

Pub Date : 2024-11-13 DOI: 10.1016/j.ympev.2024.108233

Susette Castañeda-Rico , Jesús E. Maldonado , Melissa T.R. Hawkins , Cody W. Edwards

Neotomine rodents (Cricetidae, Neotominae) represent one of the most commonly encountered and diverse group of rodents in North America, yet phylogenetic relationships within this group remain uncertain. This subfamily is known for its rapid evolution, adding more complexity to our efforts to unravel their evolutionary history. The main debate revolves around the recognition of the genus Peromyscus as monophyletic or paraphyletic due to its relationship with other genera such as Habromys, Megadontomys, Podomys, Neotomodon, and Osgoodomys. Here, we aim to resolve phylogenetic relationships within Neotominae, to further explore their evolutionary history and taxonomic boundaries. We used target capture and high-throughput sequencing of complete mitogenomes and thousands of genome-wide ultraconserved elements loci (UCEs). Our comprehensive analyses encompassed 53 species of Neotominae spanning 12 previously described genera, along with one yet-undescribed genus. We also investigated 12 out of the 13 species groups within Peromyscus. Our analyses, including Maximum Likelihood and Bayesian Inference with both mitogemomes and UCEs, as well as the coalescent species-tree-based approach with UCEs, consistently recovered concordant and well-resolved phylogenies with high levels of nodal support. We identified seven main clades within Neotominae that could potentially be recognized at the generic level, mostly to categorize the genus Peromyscus as a monophyletic group, including one species group within “Peromyscus”. Furthermore, our divergence dating estimates place the crown age of Neotominae to be around the late Miocene at ca. 7.9 – 10.7 mya. While generic level diversification continued through the Pliocene, species level diversification predominantly occurred during the late Pliocene, extending through the Pleistocene and Holocene. These epochs have been recognized as periods with significant changes in flora and fauna, driving ecological transformations on a global scale. We hypothesized that climatic and vegetation shifts during the Neogene and Quaternary, coupled with geological events, topographical features, and the presence of biogeographical corridors played a pivotal role in the speciation and diversification of Neotominae. Recognizing the importance of generating genomic-scale data coupled with a broad taxonomic sampling, our study, for the first time, offers resolution of the relationships among the main lineages of Neotominae. We expect that the phylogeny presented here will serve as a foundational resource for future systematic and evolutionary studies. This includes facilitating a proper comprehensive taxonomic revision of the group and the formal description and naming of new genera.

新啮齿目啮齿动物（Cricetidae，Neotominae）是北美洲最常见和最多样化的啮齿动物之一，但该亚科内部的系统发育关系仍不确定。该亚科以进化迅速而著称，这给我们揭示其进化历史的工作增添了更多的复杂性。主要的争论围绕着 Peromyscus 属是单系还是旁系的问题，因为它与其他属（如 Habromys、Megadontomys、Podomys、Neotomodon 和 Osgoodomys）的关系。在这里，我们的目的是解决新齿兽科内部的系统发育关系，以进一步探索其进化历史和分类界限。我们对完整的有丝分裂基因组和数千个全基因组超保守元件位点（UCEs）进行了目标捕获和高通量测序。我们的综合分析涵盖了新齿兽科的 53 个物种，跨越了 12 个以前描述过的属，以及一个尚未描述过的属。我们还调查了 Peromyscus 中 13 个物种群中的 12 个。我们的分析包括使用线粒体和 UCEs 的最大似然法和贝叶斯推断法，以及使用 UCEs 的基于物种树的聚合法，这些方法一致地恢复了具有较高节点支持度的一致且清晰的系统发生。我们在新齿兽科（Neotominae）中发现了七个主要支系，这些支系有可能在属一级得到承认，其中大部分支系将鲈属归为单系群，包括 "鲈属 "中的一个种群。此外，根据我们对分歧年代的估算，Neotominae 的冠龄约为中新世晚期的 7.9 - 10.7 米。7.9 - 10.7 mya。属级的多样化一直持续到上新世，而种级的多样化则主要发生在上新世晚期，并延续到更新世和全新世。这些时代被认为是动植物发生重大变化的时期，推动了全球范围的生态变革。我们假设，新近纪和第四纪的气候和植被变化，加上地质事件、地形特征和生物地理走廊的存在，在新齿兽科动物的物种形成和多样化过程中起到了关键作用。我们认识到生成基因组规模的数据以及广泛的分类取样的重要性，因此我们的研究首次解决了新齿兽科主要品系之间的关系问题。我们希望这里介绍的系统发生学将成为未来系统和进化研究的基础资源。这包括促进对该类群进行适当、全面的分类学修订，以及对新属的正式描述和命名。

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引用次数: 0

A comprehensive molecular phylogeny of the genus Sylvirana (Anura: Ranidae) highlights unrecognized diversity, revised classification and historical biogeography Sylvirana 属（Anura: Ranidae）的综合分子系统发育突显了尚未认识到的多样性、修订的分类和历史生物地理学。

IF 3.6 1区生物学 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY

Molecular Phylogenetics and Evolution

Pub Date : 2024-10-30 DOI: 10.1016/j.ympev.2024.108223

Yun-He Wu , Man-Hao Xu , Chatmongkon Suwannapoom , Sang Ngoc Nguyen , Robert W. Murphy , Theodore J. Papenfuss , Amy Lathrop , Felista Kasyoka Kilunda , Wei Gao , Zhi-Yong Yuan , Jin-Min Chen , Liang Zhang , Hai-Peng Zhao , Li-Jun Wang , Md Mizanur Rahman , Lotanna Micah Nneji , Gui-Gang Zhao , Yun-Yu Wang , Jie-Qiong Jin , Peng Zhang , Jing Che

The genus Sylvirana includes 12 species widely distributed in South China and Southeast Asia. The phylogenetic relationships and species diversity for Sylvirana and allied genera remain unresolved and controversial due to insufficient data and incomplete taxon sampling. Using a combined dataset of mitochondrial genes (16S and COI) and 101 nuclear genes obtained through the amplicon sequence capture approach, we generated the most comprehensive phylogenetic analysis for the genus Sylvirana to date, inferring diversity, phylogenetic relationships, and historical biogeography with unprecedented levels of taxon and geographic sampling. Our results conservatively reveal six undescribed species, mostly distributed in peninsular Indochina. Phylogenetic analyses strongly support the non-monophyly of Sylvirana with respect to Pterorana. Additionally, phylogenetic results place Sylvirana guentheri and Pelophylax lateralis into genus Humerana, supporting the inclusion of Hylarana latouchii, Papurana milleti, and Hylarana attigua within Pterorana + Sylvirana. The long-disputed species of Hylarana bannanica (previously Sylvirana) cluster with genus Papurana. Because the results of multiple non-monophyletic genera create taxonomic confusion, we suggest relegating all genera to subgenus rank of Hylarana. Sylvirana is a junior synonym of the Pterorana. Biogeographically, we trace the origin of Pterorana to Southeast Asia during the early Miocene, with subsequent dispersal thereafter. Our study shows that climatic changes may have profoundly influenced the diversification of Pterorana during the Miocene.

Sylvirana 属包括 12 个种，广泛分布于华南和东南亚地区。由于数据不足和类群取样不完整，Sylvirana 属及其同属的系统发育关系和物种多样性仍未得到解决并存在争议。我们利用线粒体基因（16S 和 COI）和通过扩增子序列捕获方法获得的 101 个核基因的组合数据集，对 Sylvirana 属进行了迄今为止最全面的系统发育分析，以前所未有的分类群和地理取样水平推断了其多样性、系统发育关系和历史生物地理学。我们的结果保守地揭示了六个未描述的物种，它们大多分布在印度支那半岛。系统发育分析有力地支持了 Sylvirana 与 Pterorana 的非单系关系。此外，系统发育结果将 Sylvirana guentheri 和 Pelophylax lateralis 归入 Humerana 属，支持将 Hylarana latouchii、Papurana milleti 和 Hylarana attigua 纳入 Pterorana + Sylvirana 属。争议已久的 Hylarana bannanica（以前为 Sylvirana）与 Papurana 属聚类。由于多个非单系属的结果造成了分类学上的混乱，我们建议将所有属归入 Hylarana 亚属。Sylvirana 是 Pterorana 的初级异名。在生物地理学上，我们追溯到 Pterorana 在中新世早期起源于东南亚，随后扩散到世界各地。我们的研究表明，气候的变化可能对中新世期间翼手目的多样化产生了深远的影响。

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引用次数: 0

Whole genome data confirm pervasive gene discordance in the evolutionary history of Coenonympha (Nymphalidae) butterflies 全基因组数据证实了蛱蝶科（Coenonympha）蝴蝶进化史中普遍存在的基因不一致现象。

IF 3.6 1区生物学 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY

Molecular Phylogenetics and Evolution

Pub Date : 2024-10-28 DOI: 10.1016/j.ympev.2024.108222

Matthew P. Greenwood , Thibaut Capblancq , Niklas Wahlberg , Laurence Després

Phylogenetic inference is challenged by genealogical heterogeneity amongst molecular markers. Such discordance is driven predominantly by incomplete lineage sorting (ILS) and interspecific gene flow, and bears attendant consequences for the accurate resolution of species relationships. Understanding the distribution of gene conflict in organismal genomes is, therefore, a key aspect of phylogenetic analysis. In this study, three large phylogenomic datasets (i.e., whole mitogenomes, conserved nuclear protein-coding loci, and genomic windows) are used to probe the extent to which discordance pervades the unresolved phylogeny of Coenonympha (Nymphalidae) butterflies. Gene tree discordance is found to be elevated at multiple historically recalcitrant phylogenetic positions. In particular, species relationships near the crown of Coenonympha and within a rapidly diversifying subclade (the hero group) remain difficult to resolve, suggesting that ILS and gene flow have obscured the evolution of this genus. These findings have implications for the taxonomy of this butterfly group and the study of its diversification history. In addition, this work lends support to a growing body of evidence that gene conflict driven by biological processes stands to confound phylogeny, even when extensive data are used.

系统发育推断受到分子标记间系谱异质性的挑战。这种不一致性主要是由不完全世系分选（ILS）和种间基因流动造成的，并对物种关系的准确解析产生相应的影响。因此，了解生物基因组中基因冲突的分布是系统发育分析的一个关键方面。本研究利用三个大型系统发生组数据集（即全有丝分裂基因组、保守的核蛋白编码位点和基因组窗口）来探究蛱蝶科（Coenonympha）蝴蝶未解决的系统发生中的不一致程度。研究发现，在多个历史上难以解决的系统发育位置上，基因树的不一致性较高。特别是，蝶冠附近的物种关系和一个快速多样化的亚支系（英雄群）内的物种关系仍然难以解决，这表明ILS和基因流掩盖了该属的进化。这些发现对该蝶类的分类学及其多样化历史的研究具有重要意义。此外，这项工作还为越来越多的证据提供了支持，这些证据表明，即使使用了大量数据，由生物过程驱动的基因冲突也会混淆系统发生学。

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引用次数: 0

Genomic and transcriptomic perspectives on the origin and evolution of NUMTs in Orthoptera 从基因组和转录组角度看直翅目 NUMTs 的起源和进化。

IF 3.6 1区生物学 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY

Molecular Phylogenetics and Evolution

Pub Date : 2024-10-23 DOI: 10.1016/j.ympev.2024.108221

Xuanzeng Liu , Nian Liu , Xuan Jing , Hashim Khan , Kaiyan Yang , Yanna Zheng , Yimeng Nie , Hojun Song , Yuan Huang

Nuclear mitochondrial pseudogenes (NUMTs) result from the transfer of mitochondrial DNA (mtDNA) to the nuclear genome. NUMTs, as “frozen” snapshots of mitochondria, can provide insights into diversification patterns. In this study, we analyzed the origins and insertion frequency of NUMTs using genome assembly data from ten species in Orthoptera. We found divergences between NUMTs and contemporary mtDNA in Orthoptera ranging from 0 % to 23.78 %. The results showed that the number of NUMT insertions was significantly positively correlated with the content of transposable elements in the genome. We found that 39.09 %-68.65 % of the NUMTs flanking regions (2,000 bp) contained retrotransposons, and more NUMTs originated from mitochondrial rDNA regions. Based on the analysis of the mitochondrial transcriptome, we found a potential mechanism of NUMT integration: mitochondrial transcripts are reverse transcribed into double-stranded DNA and then integrated into the genome. The probability of this mechanism occurring accounts for 0.30 %-1.02 % of total mitochondrial nuclear transfer events. Finally, based on the phylogenetic tree constructed using NUMTs and contemporary mtDNA, we provide insights into ancient evolutionary events such as species-specific “autaponumts” and “synaponumts” shared among different species, as well as post-integration duplication events.

核线粒体假基因（NUMTs）是线粒体DNA（mtDNA）转移到核基因组的结果。NUMTs作为线粒体的 "冷冻 "快照，可以让人们深入了解线粒体的多样化模式。在这项研究中，我们利用直翅目 10 个物种的基因组组装数据分析了 NUMTs 的起源和插入频率。我们发现 NUMTs 与直翅目当代 mtDNA 之间的差异从 0 % 到 23.78 % 不等。结果表明，NUMT插入的数量与基因组中转座元件的含量呈显著正相关。我们发现，39.09%-68.65%的NUMTs侧翼区域（2000 bp）含有反转座子，更多的NUMTs来源于线粒体rDNA区域。根据对线粒体转录本组的分析，我们发现了 NUMT 整合的潜在机制：线粒体转录本反向转录为双链 DNA，然后整合到基因组中。这种机制发生的概率占线粒体核转移事件总数的 0.30%-1.02%。最后，根据利用 NUMTs 和当代 mtDNA 构建的系统发生树，我们深入了解了古老的进化事件，如不同物种之间共享的物种特异性 "自聚体 "和 "合聚体"，以及整合后的复制事件。

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引用次数: 0